The Choice: An Order 66 Story
by ImaginIsa
Summary: "Execute Order 66." Except some clones didn't. Rex didn't, couldn't. It was wrong...he knew it was wrong...but he was bred to obey, bred to be a soldier... A story about Captain Rex, his squad, and the day that the Republic died.
**Author's Note:** I do not own Star Wars, Clone Wars, Rebels or any associated characters and locations. This story is meant to bridge the gap between Clone Wars and Rebels. And answer my own yearning to know how the clones of Torrent Company reacted to losing both Snips and Sky-Guy.

 **The Choice**

A familiar chuckle filled the silence in the darkened medical bay. CT-7567, known as Captain Rex, opened his eyes slowly – pulling himself out of the deep sleep with difficulty. General Anakin Skywalker stood above him, one side of his mouth pulled up into that crooked smile that Rex had seen so often as Anakin looked at Ashoka Tano or Senator Padme Amidala. A smile that meant " _that was a close one,"_ and something very close to _"I love you."_ It was a smile that Anakin reserved for his friends.

"I thought I lost you for a moment there, Rex," said Anakin. He sat in a chair beside Rex's bed and leaned back.

"I'm tougher than that, sir," Rex whispered. Everything hurt. Even breathing.

Anakin's smile slipped as his eyes scanned the beeping equipment above Rex's head. "I wanted them to put you straight into the bacta tank, but some of the others…"

"I'll live, sir," interjected Rex, trying to make his voice sound stronger. "It's more important for the critically wounded to get inside the tanks."

Anakin shook his head slightly. "When are you going to take care of yourself, Rex?"

"When you do, sir," Rex answered instantly.

Anakin chuckled again. "Guess that's true," he mused. "I'm not the best role model…" Something dark and angry flashed across his face but he quickly hid it. Rex felt his own stomach churn uncomfortably; he knew both of their thoughts had strayed instantly to Ashoka. Anakin's old padawan – now gone, disappeared. An ex-Jedi somewhere in the big, dangerous galaxy on her own.

Anakin visibly pulled his thoughts away from her and said, "I have some good news."

Rex tried to nod and ended up wincing instead. Anakin noticed, but did Rex the courtesy of pretending he hadn't and said, "We got Dooku."

Rex instantly sat up a little straighter. "He's captured?"

Anakin got a strange look in his eye as he replied, "He's dead."

Instantly, a cheer rose up in the med bay as the wounded members of the 501st revealed that they hadn't been sleeping at all.

"Finally!"

"The bastard's dead!"

"Someone break out the drinks!"

Jesse's comment drew ragged laughter from the wounded men, all of them feeling better with the knowledge that the terrible battle to get back the Chancellor had been worth it.

"Think they'll actually let us drink in here?" Gregor – a new addition to the team – asked seriously. More laugher followed this comment.

"Who killed him?" Rex asked.

"I did," Anakin said quietly. Instantly, the cheering began again, the clones all immensely proud of their General. But Rex knew Anakin Skywalker. Probably knew him better than even Ashoka – almost as well as Obi Wan Kenobi. Rex saw the guilt, the self-doubt, behind this revelation.

"Anakin," Rex said in a low voice. "What is it?"

Anakin's eyes widened a little at the use of his first name – not General, not sir but _Anakin_ – and then he looked away, his eyes taking in the wounded men, the medical equipment, before coming to rest once more on his second-in-command. "Killing an unarmed man…it's not the Jedi way."

"Maybe not, sir," said Rex, still speaking quietly so that the other men couldn't hear. "But you once told me that our job is to save as many people as possible. Dooku was too dangerous to leave alive. And," here Rex allowed himself a small, but dangerous smile, "If I'd been there I would have killed him myself."

Some of the guilt seemed to leave Anakin's eyes and he clapped Rex on the shoulder – but gently, as to not further aggravate Rex's injuries. "You'll have to get the next one, Rex," Anakin said.

"Not likely," Wolffe spoke up from the other side of the room. Although not part of Torrent Company, he had participated in the battle and was holed up in the medical bay with the rest of them. "General Obi Wan Kenobi and Commander Cody are taking care of Grievous as we speak. I heard a couple of the newly discharged men talking about it as they walked by this morning." The room let out a disappointed groan.

"Knowing Obi Wan," said Anakin smugly. "We may have to go and rescue him."

"Maybe wait until we're back on our feet, sir," commented Rex mildly. "Or who is going to rescue you?"

The room roared with laughter and Anakin shook his head. "I've been forced to promote Appo until you get your shot at that bacta tank, Rex. Don't keep me waiting."

"Don't worry, sir," said Rex. "I'll – we'll – be back soon."

Anakin suddenly looked really serious, and something like a chill went down Rex's spine. But that was ridiculous. "Thank you, Rex," said Anakin seriously. He raised his voice a bit and said, "Thank you, everyone. I don't know how we could have survived these last few years if you hadn't been around."

"It has been our pleasure, sir," responded Rex. "You…we got a good General." The rest of Torrent Company nodded. Wolffe and Gregor – the only non-501st clones in the room – looked on curiously, but didn't disagree. They had heard the stories. All of the Grand Army had heard the stories. And here was General Skywalker visiting his men while they were injured; the stories, then, at least in part, were true.

Anakin gave Rex his lopsided smile, a salute and walked out.

 _ **Order 66: The Jedi Council has been deemed an enemy of the Republic. Kill all Jedi on sight.**_

The droid surgeon entered the med-bay room that held the newly-recovered members of Torrent Company plus Gregor and Wolffe. It placed a covered tray in the center of the room and looked up at Captain Rex. Rex, about halfway through putting on his armor, paused. The droid looked – there was no other word for it – grave.

"You were right," the droid told him in its metallic, sing-song voice. "You all had them." The droid uncovered the tray and the room went silent. Ten petri dishes stood out against the silver – petri dishes that held small electronic chips surrounded by brain matter. Each of them were labeled with the number of the clone from whom they had been extracted.

"You were telling the truth," said Jesse in awe. "They were really in there."

"No," said Rex grimly. "Fives was telling the truth."

"We don't actually know that," said Wolffe gruffly. He had been the least willing to take matters into their own hands and have the chips extracted. Rex had spent several hours with nothing to do except sit around and think, and he had finally decided to act on the overwhelming feeling he had to prove Fives right. The rest of the group in the med-bay were no strangers to bending the rules – they were General Skywalker's squad after all – and they had all been a part of that terrifying mission to Umbara when they had stood up to General Krell. All of them, that is, except for Gregor and Wolffe. Gregor didn't like the idea of anyone messing with his mind or memory and had been eager to have the chip removed. Wolffe had taken some more convincing. Almost two hours of it, in fact. But, with the help of the others, he had. The droid-surgeon had been sworn to secrecy and the chips had been removed.

"For all we know," Wolffe continued. "Those really were keeping us from going crazy and we've sealed our own fates."

"I don't know," Kix said. "I feel…I don't know…more free. It's as this annoying voice in the back of my head was finally turned off."

"I know exactly what you mean," agreed Zeere.

Rex turned to the Surgeon. "Hide those in a safe location. Do not speak of this to anyone or show them to anyone unless I am with them, do you understand?"

"This is a hospital," the droid complained. "Not a safety deposit box."

"Listen here, tinny," Rex growled. "I've killed more droids these past three years than you've ever seen in your life. Do as I say. The safety of the Republic is at stake."

The Surgeon made a worried noise and said, "Of course…I know just the place. No one ever uses the maternity ward in this hospital – all we ever get are clones. I'll hide them somewhere in there."

"As long as it's secure," Rex insisted. Then he turned to the rest of the squad; "Come on, men. Let's go find our General."

Outside of the hospital, it was weirdly quiet. It was Coruscant – filled with the bustling of traffic from millions of beings and news blaring from every sign – yet something felt _wrong._

"What the hell is going on?" someone muttered.

"SIR!" Gregor suddenly yelled, pointing. Everyone turned. And Rex wondered what nightmare he had stepped into. Because, there in the distance, the Jedi Temple was on fire. They started running. Wolffe jumped into the driver's seat of a medical shuttle – the driver's protests fell on deaf ears – and they all jumped on. A few minutes later, they landed in front of the Temple.

Appo calmly walked out to meet them. "Hello, everyone, did you just get discharged?"

"Lieutenant Appo..!" Rex began.

"It's Commander, now, actually," Appo said, "I got a special promotion in the face of Order 66."

Rex stopped breathing.

"Wh…what?" Rex choked out.

"Order 66," Appo repeated calmly. "The Jedi tried to attack the Chancellor. We were able to stop them without too much trouble – seems as if they were never expecting us to find out about…"

Rex had pushed past him, rushed into the Temple, and stopped again. The others were right behind him. He heard Jesse gasp. But the others had the good sense to turn off the external speakers on their helmets.

They were all dead. Jedi Knights in flowing robes, the Temple Guards with their strange headdresses and long lightsabers, and…and…and the _younglings._ Most of them too young for lightsabers. Many of them huddled together for safety. And many of them with – a cold horror filled Rex from deep within his core – many of them with lightsaber burns.

Boil took off his helmet and ran behind a pillar to be sick.

Kix opened up a private channel with Rex over their coms and said in a halting, tear-filled voice, "What happened here? Rex, _what happened here!?"_

"I don't…" Rex couldn't even get out the words.

" _Fierfek,_ " Wolffe swore, joining the channel. "Rex, you were right. That thing in our heads…it must have…"

"You tried to warn us, Fives," Rex said in a daze. _He could hear his brother screaming at them that he wasn't crazy right before he was gunned down._ "You tried to warn us."

"Hey," Appo said, walking up to them with a worried expression. "Are you all okay? It's disgusting that they tried to betray us but we got them in time. You should hear some of the plans the Emperor has…and, guess what? General Skywalker knew all along."

"What?" asked Rex sharply.

"General Skywalker is on the Emperor's side," Appo explained. "He's off hunting separatist leaders right now but when he gets back he's going to help with re-organizing what's left of the Jedi. They're talking about plans for the future of the Imperial Army…really big stuff. We're lucky to have been under him for the entire war. We're probably going to get recognized for our heroics now that the war is over."

Rex couldn't believe it. Didn't understand. How could Appo continue talking as if all this were _normal_? How could General Skywalker – Anakin, his friend – have been working with the Emperor to cause all of this destruction. Rex looked around him at the carnage and found himself wishing, for a moment, that he had left in that damn inhibitor chip. So that he could go on like Appo was now. See all of this as just another casualty of war. Not realizing that they had been, as Krell had once said, nothing but pawns.

Torrent Company tried to pretend. For two weeks they tried to pretend that everything was fine. They assisted with the clean-up of the Temple, patrolled the streets of Coruscant and the Senate buildings, and followed orders. More than once, Rex woke up in the middle of the night to one or the other of his friends crying out in their sleep. Boil in particular – who had always had a soft-spot for younglings – had night terrors that left him crying silently in the dark. But, at the two week mark, Darth Vader came to address the 501st.

It was before the speech, Rex and the others were walking towards the parade grounds with their armor newly shined, when Darth Vader himself walked by. And Rex _knew._ He knew from the very moment that he saw the Sith that it was no one but…

"Anakin!"

Darth Vader paused in mid-stride. The entire company and anyone else who happened to be standing about froze where they stood.

Darth Vader turned slowly and that black helmet reflected Rex' tired face back at him. A dread he had never associated with Anakin Skywalker – Ashoka's Sky-Guy, Padme's Annie, Obi-Wan's old padawan – crept down his spine.

But Rex _knew._ Somehow he knew – there had been something in the walk, something in the almost casual way the Sith had turned that helmeted head towards the window that led to the starships.

"General Skywalker?" Rex asked, more quietly. "That is you, right?"

Lord Vader stared at him in silence for a moment. No, not silence. The awful sound of that respirator filled the otherwise silent hall as everyone else held their breath and wondered if Rex was about to get himself killed.

"Captain Rex…" Vader said. "You are…mistaken. Anakin Skywalker is dead. He died with the Jedi. There is now only the Dark Side."

Vader continued down the hallway, everyone standing at attention as he passed. Rex was frozen where he stood. And Boil let out a small whimper in the background.

"All those younglings," Jesse said in horror. "Those cut down by lightsabers…"

"Shut up!" Rex snapped over his shoulder. He put on his helmet and let the tears stream silently down his cheeks but still, he said, "Shut up! We're soldiers. We follow orders…"

Jesses roughly pulled his own helmet over his head and hissed back at him, over the com, "But we didn't. But we…Rex, we _know._ "

"I know, brother," Rex whispered back. "I know."

He cried during the entirely of the speech that day.

Within the month, almost every member of Torrent Company had died in engagements with surviving Jedi. The rumor started that they often let themselves be killed rather than use deadly force against the once protectors of peace. Within two months, Rex – along with Wolffe and Gregor – were given an honorable discharges. The notice was signed by Lord Vader himself. Rex wondered if Vader knew they had removed their chips. He decided it didn't matter. The Republic they had served was gone. Now, there was only the Empire.

 **Additional Author's Note:** If you like my style, check out my short story "The Beginning of the End" about when Ashoka leaves the Jedi. If you don't mind original characters and love Clone War Era stories, check out my story "The Satellite." Please review!


End file.
